Evolutionary and functional genomics of genetic novelties and expression adaptation in Drosophila

适应性转录组进化可能是所有适应的重要组成部分。在此，我提议 用果蝇研究两种主要的转录组进化。首先，我们将识别基因新奇， 重点是生殖组织，包括单细胞水平的分析。然后我们将调查 利用包括CRISPR在内的各种遗传和生物化学工具， 和RNAi来了解作用于这些新奇事物的选择因子。第二，我们将利用人口 表征有助于物种内局部适应的适应性转录组差异的方法， 和转录组适应在物种之间更长的时间尺度。然后我们将使用这些结果来推断 转录组的部分适应性地为多种组织和物种进化。我们将使用基因和 ATAC-seq实验，以研究收敛表达适应是否通常具有共享的 遗传基础或适应是否通常通过不同物种的不同轨迹进行。

Adaptive transcriptome evolution likely underlies a substantial component of all adaptations. Here I propose to study two main types of transcriptome evolution using Drosophila. First, we will identify genetic novelties, focusing on reproductive tissues, including analysis at the single-cell level. We will then investigate the functions of these novelties in two species using a variety of genetic and biochemical tools, including CRISPR and RNAi to learn about the agents of selection acting on these novelties. Second, we will use population approaches to characterize adaptive transcriptome divergence contributing to local adaptation within species, and transcriptome adaptation over longer timescales between species. We will then use these results to infer the fraction of the transcriptome evolving adaptively for multiple tissues and species. We will use genetic and ATAC-seq experiments to investigate whether convergent expression adaptation generally has a shared genetic basis or whether adaptation generally proceeds by different trajectories in different species.